Bencomia sphaerocarpa is listed on Annex II of the Habitats Directive and under Appendix I of the Convention on the Conservation of European Wildlife and Natural Habitats (Bern Convention). It is listed Critically Endangered CR D in the Spanish Red List (Moreno 2008), and as species "En peligro de extinción" in the national and regional catalogues of threatened species.

The species occurs within the protected area Parque Rural de Frontera (SCI). Seeds from every subpopulation have been collected and stored in the germplasm bank Banco de Germoplasma del Jardín Botánico Viera y Clavijo. A monitoring programme has been developed for the subpopulation in Fileba and 20 individuals have been re-introduced in Tábano. Both subpopulations are considered the most threatened and have been fenced (Martín Osorio et al. 2004).

In order to ensure the conservation of the species grazing exclusion zones must be designated, the activities of reintroduction, reinforcement or transfer of individuals must be kept in place, disease control programmes have to be implemented and population monitoring and research in reproductive dynamics have to be developed.